bugrelax - Bugs: bug #20185, The relax online HTML manual is...

 
 
Show feedback again

bug #20185: The relax online HTML manual is broken.

Submitted by:  Edward d Auvergne <bugman>
Submitted on:  Wed 19 Sep 2012 03:33:33 PM UTC  
 
Category: Web pages (HTML)Specific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.1.0Operating System: None

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

Tue 16 Oct 2012 08:19:57 AM UTC, SVN revision 17828:

Merged revisions 17391-17538 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r17391 | bugman | 2012-08-30 11:02:04 +0200 (Thu, 30 Aug 2012) | 3 lines

Added a paragraph to the model-free chapter of the user manual explaining the J(w) equation forms.
........
r17392 | bugman | 2012-08-30 11:03:23 +0200 (Thu, 30 Aug 2012) | 3 lines

Fixed some citations in the newly introduced model-free J(w) paragraph.
........
r17393 | bugman | 2012-08-30 11:13:54 +0200 (Thu, 30 Aug 2012) | 3 lines

Added a LaTeX label to the NOE chapter of the user manual.
........
r17394 | bugman | 2012-08-30 11:14:21 +0200 (Thu, 30 Aug 2012) | 3 lines

Fixes for the referencing in the J(w) mapping chapter of the user manual.
........
r17395 | bugman | 2012-08-30 16:40:40 +0200 (Thu, 30 Aug 2012) | 3 lines

Small description edit for the relax_data.temp_control user function.
........
r17396 | bugman | 2012-08-30 16:42:48 +0200 (Thu, 30 Aug 2012) | 3 lines

Spell fix for the relax_data.temp_calibration user function description.
........
r17397 | bugman | 2012-08-30 16:49:41 +0200 (Thu, 30 Aug 2012) | 3 lines

Fix for the incomplete relax_data.temp_control user function description.
........
r17398 | bugman | 2012-08-30 16:50:46 +0200 (Thu, 30 Aug 2012) | 3 lines

Another fix for the relax_data.temp_control description.
........
r17399 | bugman | 2012-08-30 17:43:09 +0200 (Thu, 30 Aug 2012) | 3 lines

Added the Viles et al., 2001 reference.
........
r17400 | bugman | 2012-08-30 18:07:51 +0200 (Thu, 30 Aug 2012) | 5 lines

Added a new section called 'From spectra to peak intensities' to the Rx fitting chapter of the manual.

This adds a number of recommendations for high quality relaxation rates.
........
r17401 | bugman | 2012-08-30 18:11:27 +0200 (Thu, 30 Aug 2012) | 3 lines

The NOE chapter now points to the recommendations in the Rx fitting chapter.
........
r17402 | bugman | 2012-08-30 18:11:49 +0200 (Thu, 30 Aug 2012) | 3 lines

[...]

[...] Added the nth package for the user manual LaTeX compilation.

[...]........

[...] r17403 | bugman | 2012-08-31 22:05:56 +0200 (Fri, 31 Aug 2012) | 6 lines

[...]

[...] Bug fix for the loading of peak intensities via spectrum.read_intensities.

[...]

[...] The user function could not be applied twice, preventing the loading of data from different spin

[...] systems such as Trp indole NH data.

[...]........

[...] r17404 | bugman | 2012-08-31 22:16:37 +0200 (Fri, 31 Aug 2012) | 6 lines

[...]

[...] Bug fix for the reading of Sparky peak lists.

[...]

[...] Spin names with numbers at the end were not being correctly identified. This fix allows Trp indole

[...] NE1-HE1 data to be loaded.

[...]........

[...] r17405 | bugman | 2012-08-31 23:35:22 +0200 (Fri, 31 Aug 2012) | 3 lines

[...]

[...] Allowed the raggedbottom LaTeX setting as this is better for the screenshot layout in the user manual.

[...]........

[...] r17406 | bugman | 2012-08-31 23:36:07 +0200 (Fri, 31 Aug 2012) | 3 lines

[...]

[...] Added some Sparky info to the Rx curve-fitting chapter of the user manual.

[...]........

[...] r17407 | bugman | 2012-08-31 23:36:17 +0200 (Fri, 31 Aug 2012) | 3 lines

[...]

[...] Added a section label.

[...]........

[...] r17408 | bugman | 2012-08-31 23:42:01 +0200 (Fri, 31 Aug 2012) | 5 lines

[...]

[...] Added a step-by-step tutorial for the GUI NOE auto-analysis to the user manual.

[...]

[...] This includes 22 screenshots of all the steps!

[...]........

[...] r17409 | bugman | 2012-08-31 23:53:41 +0200 (Fri, 31 Aug 2012) | 3 lines

[...]

[...] Modified the NOE sample script to include Trp indole NH data.

[...]........

[...] r17410 | bugman | 2012-09-01 10:09:08 +0200 (Sat, 01 Sep 2012) | 6 lines

[...]

[...] Added some Trp peak data (backbone and indole N) to the Sparky steady-state NOE peak lists.

[...]

[...] This is in preparation for the modification of the NOE system test to catch bug #20119

[...] (https://gna.org/bugs/index.php?20119).

[...]........

[...] r17411 | bugman | 2012-09-01 10:17:30 +0200 (Sat, 01 Sep 2012) | 5 lines

[...]

[...] Modified the NOE system test to test the usage of Trp indole 15N data.

[...]

[...] This is to catch bug #20119 (https://gna.org/bugs/index.php?20119).

[...]........

[...] r17412 | bugman | 2012-09-01 10:18:22 +0200 (Sat, 01 Sep 2012) | 5 lines

[...]

[...] Significant update of the NOE chapter of the user manual.

[...]

[...] The sample script used in this chapter was incredibly out of date!

[...]........

[...] r17413 | bugman | 2012-09-01 11:05:16 +0200 (Sat, 01 Sep 2012) | 3 lines

[...]

[...] Lots of editing of the NOE chapter of the user manual.

[...]........

[...] r17414 | bugman | 2012-09-01 11:20:30 +0200 (Sat, 01 Sep 2012) | 3 lines

[...]

[...] Modified the NOE system test to catch bug #20120 (https://gna.org/bugs/?20120).

[...]........

[...] r17415 | bugman | 2012-09-01 11:21:54 +0200 (Sat, 01 Sep 2012) | 3 lines

[...]

[...] Removed a debugging print out.

[...]........

[...] r17416 | bugman | 2012-09-01 11:27:10 +0200 (Sat, 01 Sep 2012) | 6 lines

[...]

[...] Fix for bug #20120 (https://gna.org/bugs/?20120), the bad Grace plots with multiple spin types.

[...]

[...] The grace data assembly function was not setting the correct index for when a spin type changes to a

[...] preexisting type.

[...]........

[...] r17417 | bugman | 2012-09-01 13:13:01 +0200 (Sat, 01 Sep 2012) | 6 lines

[...]

[...] Bug fix for the generic_fns.grace.get_data() function.

[...]

[...] This was just recently introduced and was triggered by the Relax_fit.test_bug_12670_12679 system

[...] test.

[...]........

[...] r17418 | bugman | 2012-09-01 14:58:49 +0200 (Sat, 01 Sep 2012) | 5 lines

[...]

[...] Created the GUI wizard _apply() method for executing the current page's _apply() method.

[...]

[...] This is for the GUI tests to simulate a click on the 'Apply' button.

[...]........

[...] r17419 | bugman | 2012-09-01 15:13:43 +0200 (Sat, 01 Sep 2012) | 5 lines

[...]

[...] The spectrum.read_intensities user function now prints out a list of the intensities read in.

[...]

[...] This is for better user feedback as to what the user function has actually done.

[...]........

[...] r17420 | bugman | 2012-09-01 15:14:32 +0200 (Sat, 01 Sep 2012) | 3 lines

[...]

[...] The NOE auto-analysis GUI test now checks the support for Trp indole N data as well.

[...]........

[...] r17421 | bugman | 2012-09-03 10:19:35 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Fix for the spin.create user function documentation - the prompt examples were wrong.

[...]........

[...] r17422 | bugman | 2012-09-03 10:23:39 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Created a directory for screenshots of the spin viewer window operation.

[...]........

[...] r17423 | bugman | 2012-09-03 10:48:57 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Changed the "View->Spin view" menu item to "View->Spin viewer".

[...]........

[...] r17424 | bugman | 2012-09-03 11:11:48 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Shifted the spin viewer screenshots into their own directory.

[...]........

[...] r17425 | bugman | 2012-09-03 11:16:01 +0200 (Mon, 03 Sep 2012) | 5 lines

[...]

[...] Redesign of the data model chapter of the user manual.

[...]

[...] This includes the moving of all of the spin viewer window text and screenshots from the NOE chapter.

[...]........

[...] r17426 | bugman | 2012-09-03 11:28:42 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added screenshots of the spin viewer spin loading wizard sequence.read page.

[...]........

[...] r17427 | bugman | 2012-09-03 11:43:36 +0200 (Mon, 03 Sep 2012) | 6 lines

[...]

[...] More rearrangements of data model and NOE chapters of the relax manual.

[...]

[...] The GUI spin deselection part of the NOE chapter has been shifted into the data model chapter. And

[...] the GUI loading of spins from a sequence file section has been completed.

[...]........

[...] r17428 | bugman | 2012-09-03 12:06:00 +0200 (Mon, 03 Sep 2012) | 6 lines

[...]

[...] Defined a new set of LaTeX commands for prompt/script/GUI strings and elements for the user manual.

[...]

[...] These will be used to regularize the text throughout the manual, as this is currently quite mixed

[...] up.

[...]........

[...] r17429 | bugman | 2012-09-03 12:16:00 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added some more LaTeX functions for formatting consistency.

[...]........

[...] r17430 | bugman | 2012-09-03 13:29:09 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Removed some '()' text from the end of the user functions in the user function documentation.

[...]........

[...] r17431 | bugman | 2012-09-03 14:13:37 +0200 (Mon, 03 Sep 2012) | 6 lines

[...]

[...] Improved the consistency on the user manual by using the new LaTeX commands.

[...]

[...] These changes are throughout the manual and affect all the text of user functions, menu items,

[...] prompt examples, GUI elements, files, directories, etc.

[...]........

[...] r17432 | bugman | 2012-09-03 14:22:16 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Clean up of a paragraph of the data model chapter of the user manual.

[...]........

[...] r17433 | bugman | 2012-09-03 14:24:13 +0200 (Mon, 03 Sep 2012) | 6 lines

[...]

[...] Changed the order of the Rx curve-fitting and NOE chapters in the relax manual.

[...]

[...] This is because the NOE chapter references passages from the Rx curve-fitting chapter, so it's more

[...] logical to have the Rx curve-fitting chapter first.

[...]........

[...] r17434 | bugman | 2012-09-03 14:51:11 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Fix for the Farrow et al., 1995 DOI number.

[...]........

[...] r17435 | bugman | 2012-09-03 15:03:36 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added the Fushman et al., 1998 reference.

[...]........

[...] r17436 | bugman | 2012-09-03 15:06:25 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added the other consistency testing references to the citation chapter of the manual.

[...]........

[...] r17437 | bugman | 2012-09-03 15:06:52 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added a LaTeX label to the J(w) mapping chapter.

[...]........

[...] r17438 | bugman | 2012-09-03 15:13:16 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Activated the consistency testing chapter of the user manual.

[...]........

[...] r17439 | bugman | 2012-09-03 15:13:38 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Large edits of the consistency testing chapter of the user manual.

[...]........

[...] r17440 | bugman | 2012-09-03 17:37:14 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Added trp indole NH loading into the relaxation curve-fitting sample script.

[...]........

[...] r17441 | bugman | 2012-09-03 22:34:03 +0200 (Mon, 03 Sep 2012) | 6 lines

[...]

[...] Editing of the relaxation curve-fitting and NOE chapters of the user manual.

[...]

[...] This is to synchronise the format of the two chapters, and includes the swapping of text between

[...] them.

[...]........

[...] r17442 | bugman | 2012-09-03 23:07:07 +0200 (Mon, 03 Sep 2012) | 3 lines

[...]

[...] Small edits of the relax data model chapter of the user manual.

[...]........

[...] r17443 | bugman | 2012-09-04 11:52:07 +0200 (Tue, 04 Sep 2012) | 3 lines

[...]

[...] Added some Grace plots from an NOE analysis for use in the user manual.

[...]........

[...] r17444 | bugman | 2012-09-04 16:51:24 +0200 (Tue, 04 Sep 2012) | 5 lines

[...]

[...] Added a tonne of GUI screenshots of an R1 analysis.

[...]

[...] These will be used in the relaxation curve-fitting chapter of the user manual.

[...]........

[...] r17445 | bugman | 2012-09-04 16:51:25 +0200 (Tue, 04 Sep 2012) | 7 lines

[...]

[...] Large expansion and lots of editing of the relaxation curve-fitting chapter of the user manual.

[...]

[...] The GUI section has been added which includes step-by-step instructions on how to use relax,

[...] illustrated with screenshots at each step. There has been general editing of the whole of the

[...] chapter as well.

[...]........

[...] r17446 | bugman | 2012-09-04 16:52:00 +0200 (Tue, 04 Sep 2012) | 3 lines

[...]

[...] Editing of the relax data model chapter of the user manual.

[...]........

[...] r17447 | bugman | 2012-09-04 16:52:34 +0200 (Tue, 04 Sep 2012) | 3 lines

[...]

[...] The old R1 and R2 analysis screenshots have been shifted to the intro chapter.

[...]........

[...] r17448 | bugman | 2012-09-04 16:53:06 +0200 (Tue, 04 Sep 2012) | 3 lines

[...]

[...] Some editing of the NOE chapter of the relax user manual.

[...]........

[...] r17449 | bugman | 2012-09-04 17:11:43 +0200 (Tue, 04 Sep 2012) | 3 lines

[...]

[...] Fix for bug #20133 (https://gna.org/bugs/?20133) - this was simply a missing import.

[...]........

[...] r17450 | bugman | 2012-09-05 12:12:02 +0200 (Wed, 05 Sep 2012) | 3 lines

[...]

[...] Editing of the nmrPipe script in the Rx curve-fitting chapter of the manual.

[...]........

[...] r17451 | semor | 2012-09-05 13:52:36 +0200 (Wed, 05 Sep 2012) | 6 lines

[...]

[...] Added some text and a reference to the consistency testing chapter.

[...]

[...] This follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] r17452 | bugman | 2012-09-05 13:52:45 +0200 (Wed, 05 Sep 2012) | 5 lines

[...]

[...] Bug fix for the creation of 2D graphs via grace.write for when many data sets exist.

[...]

[...] The algorithm for setting the Grace symbol number to be between 1 and 10 was broken!

[...]........

[...] r17453 | semor | 2012-09-05 14:16:17 +0200 (Wed, 05 Sep 2012) | 8 lines

[...]

[...] Added text to detail the usage of the consistency testing script.

[...]

[...] This text was modified from the corresponding text for jw_mapping.

[...]

[...] This follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] r17454 | bugman | 2012-09-05 14:18:38 +0200 (Wed, 05 Sep 2012) | 3 lines

[...]

[...] Deletion of the relax version LaTeX file - this is automatically created anyway.

[...]........

[...] r17455 | semor | 2012-09-05 14:20:52 +0200 (Wed, 05 Sep 2012) | 8 lines

[...]

[...] Added the DOI to reference Morin11 and fixed indentation.

[...]

[...] 10.1016/j.pnmrs.2010.12.003

[...]

[...] This follows a comment by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00022.html

[...] (Message-id: )

[...]........

[...] r17456 | semor | 2012-09-05 14:25:48 +0200 (Wed, 05 Sep 2012) | 3 lines

[...]

[...] Made some corrections to the formatting of math symbols in Latex.

[...]........

[...] r17457 | semor | 2012-09-05 14:48:42 +0200 (Wed, 05 Sep 2012) | 8 lines

[...]

[...] Corrected the bibliography entries whih were still in plain text and not as a Latex \cite call...

[...]

[...] Also renamed the MorinGagne09 entry to MorinGagne09a as there is now also MorinGagne09b.

[...]

[...] This was proposed by Edward d'Auvergne in a post at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00025.html

[...] (Message-id: )

[...]........

[...] r17458 | semor | 2012-09-05 15:08:57 +0200 (Wed, 05 Sep 2012) | 6 lines

[...]

[...] Added a directory for placing consistency testing graphics.

[...]

[...] This follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] r17459 | semor | 2012-09-05 15:23:32 +0200 (Wed, 05 Sep 2012) | 10 lines

[...]

[...] Added a modified version of figure 1 from Morin and Gagne (JBNMR, 2009).

[...]

[...] http://dx.doi.org/10.1007/s10858-009-9381-4

[...]

[...] File formats are .agr (xmgrace), eps (gzipped), and png.

[...]

[...] This follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] r17460 | semor | 2012-09-05 15:33:12 +0200 (Wed, 05 Sep 2012) | 6 lines

[...]

[...] Added some text to describe the consistency testing example figure.

[...]

[...] This follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] r17461 | semor | 2012-09-05 16:00:48 +0200 (Wed, 05 Sep 2012) | 12 lines

[...]

[...] Added more text to describe the consistency testing approach.

[...]

[...] Also includes a very basic point by point protocol for consistency testing.

[...]

[...] This was proposed by by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00028.html

[...] (Message-id: )

[...]

[...] This also follows a discussion started by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00019.html

[...] (Message-id: )

[...]........

[...] r17462 | semor | 2012-09-05 17:02:41 +0200 (Wed, 05 Sep 2012) | 12 lines

[...]

[...] Reverted r17456.

[...]

[...] This follows a remark by Edward d'Auvergne at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00029.html

[...] (Message-id: )

[...]

[...] The command used was:

[...] svn merge -r17456:17455 .

[...]

[...] Then, the file was manually adjusted since there were apparently conflicts with svn...

[...]........

[...] r17463 | semor | 2012-09-05 17:09:25 +0200 (Wed, 05 Sep 2012) | 13 lines

[...]

[...] Added the bounding box and a centerline command to the code for the figure for consistency testing...

[...]

[...] This follows two remark by Edward d'Auvergne at:

[...]

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00030.html

[...] (Message-id: )

[...]

[...] and

[...]

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00032.html

[...] (Message-id: )

[...]........

[...] r17464 | semor | 2012-09-05 17:15:23 +0200 (Wed, 05 Sep 2012) | 3 lines

[...]

[...] Made a small correction to a reference such that a superscript is correctly displayed.

[...]........

[...] r17465 | semor | 2012-09-05 21:07:58 +0200 (Wed, 05 Sep 2012) | 7 lines

[...]

[...] Fixed a bibliography entry label problem.

[...]

[...] This was spotted by Edward d'Auvergne in a post at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00040.html

[...] (Message-id: )

[...]........

[...] r17466 | semor | 2012-09-05 21:11:24 +0200 (Wed, 05 Sep 2012) | 6 lines

[...]

[...] Fixed the bounding box for the consistency testing figure and also fixed some Latex unfriendly code...

[...]

[...] Problems were spotted by Edward d'Auvergne in a post at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00039.html

[...] (Message-id: )

[...]........

[...] r17467 | bugman | 2012-09-06 08:17:08 +0200 (Thu, 06 Sep 2012) | 3 lines

[...]

[...] Fixed the newlines in the sample script in the consistency testing chapter.

[...]........

[...] r17468 | bugman | 2012-09-06 10:59:01 +0200 (Thu, 06 Sep 2012) | 7 lines

[...]

[...] Editing of the "Values, gradients, and Hessians" chapter of the user manual to make it fit better.

[...]

[...] The context of this chapter has been specified by changing the title to "Optimisation of relaxation

[...] data -- values, gradients, and Hessians" and the intro text has been updated. As this chapter is no

[...] longer straight after the model-free chapter, this is needed.

[...]........

[...] r17469 | bugman | 2012-09-06 11:19:43 +0200 (Thu, 06 Sep 2012) | 3 lines

[...]

[...] Editing and a number of fixes/cleanups for the consistency testing chapter of the user manual.

[...]........

[...] r17470 | bugman | 2012-09-06 11:30:04 +0200 (Thu, 06 Sep 2012) | 3 lines

[...]

[...] Small edits of the consistency testing figure caption in the relax user manual.

[...]........

[...] r17471 | bugman | 2012-09-06 11:47:49 +0200 (Thu, 06 Sep 2012) | 3 lines

[...]

[...] Big clean up of the Bibtex bibliography file for the relax user manual.

[...]........

[...] r17472 | semor | 2012-09-06 11:48:22 +0200 (Thu, 06 Sep 2012) | 6 lines

[...]

[...] Added some text to explain why test only J(0) is discussed whereas the script also calculated F_R2 and F_eta.

[...]

[...] This was suggested by Edward d'Auvergne in a post at:

[...] https://mail.gna.org/public/relax-devel/2012-09/msg00044.html

[...] (Message-id: )

[...]........

[...] r17473 | bugman | 2012-09-06 16:07:04 +0200 (Thu, 06 Sep 2012) | 5 lines

[...]

[...] A few small edits of the relaxation curve-fitting chapter.

[...]

[...] This is to reinforce the exact time of the relaxation time period.

[...]........

[...] r17474 | bugman | 2012-09-06 17:14:43 +0200 (Thu, 06 Sep 2012) | 3 lines

[...]

[...] Re-added Dominique Marion's solvent suppression to the NMRPipe script in the curve-fitting chapter.

[...]........

[...] r17475 | bugman | 2012-09-07 08:59:17 +0200 (Fri, 07 Sep 2012) | 5 lines

[...]

[...] Set up the Bruker Dynamics Center system tests as GUI tests.

[...]

[...] This is in preparation for catching bug #20152 (https://gna.org/bugs/?20152).

[...]........

[...] r17476 | bugman | 2012-09-07 09:29:57 +0200 (Fri, 07 Sep 2012) | 5 lines

[...]

[...] Created the test_bug_20152_read_dc_file() GUI test for catching bug #20152 (https://gna.org/bugs/?20152).

[...]

[...] This includes truncated data taken from the bug report (with data for only the first 3 residues).

[...]........

[...] r17477 | bugman | 2012-09-07 10:21:46 +0200 (Fri, 07 Sep 2012) | 5 lines

[...]

[...] The bruker.read user function now throws a RelaxError when old PDC files are detected.

[...]

[...] This is a partial fix for bug #20152 (https://gna.org/bugs/?20152).

[...]........

[...] r17478 | bugman | 2012-09-07 10:46:18 +0200 (Fri, 07 Sep 2012) | 6 lines

[...]

[...] Bug fix for the creation of the user function GUI pages - the (a)synchronous arg is now observed.

[...]

[...] This argument was being ignored, which in some wizards was causing user function calls to be

[...] asynchronous. This can result in racing related crashes!

[...]........

[...] r17479 | bugman | 2012-09-07 10:48:15 +0200 (Fri, 07 Sep 2012) | 9 lines

[...]

[...] Bug fix for the execution of wizard pages - the execution status is now observed.

[...]

[...] This fixes bug #20152 (https://gna.org/bugs/?20152).

[...]

[...] The problem was that the execution status was being lost in the protected_exec() function. However

[...] as relax errors are caught in the GUI interpreter anyway and the status is returned normally, the

[...] protected_exec() wrapper was removed.

[...]........

[...] r17480 | bugman | 2012-09-07 11:03:10 +0200 (Fri, 07 Sep 2012) | 5 lines

[...]

[...] Modified the test_bug_20152_read_dc_file() GUI test to catch the RelaxError!

[...]

[...] This error is because of the old PDC format.

[...]........

[...] r17481 | bugman | 2012-09-17 10:51:37 +0200 (Mon, 17 Sep 2012) | 3 lines

[...]

[...] Comment spelling fix.

[...]........

[...] r17482 | bugman | 2012-09-17 13:35:40 +0200 (Mon, 17 Sep 2012) | 3 lines

[...]

[...] Changed the RelaxError for missing relaxation times in the relaxation curve-fitting analyses.

[...]........

[...] r17483 | bugman | 2012-09-17 13:58:27 +0200 (Mon, 17 Sep 2012) | 6 lines

[...]

[...] Fix for bug #20173 (https://gna.org/bugs/?20173).

[...]

[...] The palmer.create user function should have been checking that the diffusion tensor had been

[...] initialised. This is now being performed.

[...]........

[...] r17484 | bugman | 2012-09-17 16:44:01 +0200 (Mon, 17 Sep 2012) | 6 lines

[...]

[...] Proper bug fix for storing the execution status of wizard and user function pages.

[...]

[...] This allows the test suite to pass again. The execution status is now properly returned from the

[...] wizard pages run synchronously (and always set to True for asynchronous calls).

[...]........

[...] r17485 | bugman | 2012-09-17 18:05:56 +0200 (Mon, 17 Sep 2012) | 6 lines

[...]

[...] Expanded the spin ID list for the structure.load_spins user function.

[...]

[...] This now includes the spins "@N", "@NE1", "@C", "@H", "@O", "@P", ":A@C2", ":A@C8", ":G@N1",

[...] ":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5", ":U@C6".

[...]........

[...] r17486 | bugman | 2012-09-18 10:51:49 +0200 (Tue, 18 Sep 2012) | 3 lines

[...]

[...] MS Windows fix - the NOE system and GUI tests are now less strict in checking the errors.

[...]........

[...] r17487 | bugman | 2012-09-18 12:11:17 +0200 (Tue, 18 Sep 2012) | 6 lines

[...]

[...] Updated the scripting section of the intro chapter of the user manual for non-technical users.

[...]

[...] See http://www.mail-archive.com/relax-users@gna.org/msg01253.html and bug #20174

[...] (http://gna.org/bugs/?20174).

[...]........

[...] r17488 | bugman | 2012-09-18 15:19:03 +0200 (Tue, 18 Sep 2012) | 6 lines

[...]

[...] Bug fix for the repetition of Monte Carlo simulations in the relaxation curve-fitting analyses.

[...]

[...] This is in the specific analysis API, so will allow all analysis types to repeat Monte Carlo

[...] simulations for error analysis.

[...]........

[...] r17489 | bugman | 2012-09-18 16:15:01 +0200 (Tue, 18 Sep 2012) | 6 lines

[...]

[...] Created the new generic_fns.result_files for standardising the handling of results files.

[...]

[...] This fixes the bug where results files are repetitively added to the list. All of the code touching

[...] cdp.result_files now uses this module instead.

[...]........

[...] r17490 | bugman | 2012-09-18 18:15:51 +0200 (Tue, 18 Sep 2012) | 6 lines

[...]

[...] Window ordering bug fix for the user function windows launched from the spin viewer window.

[...]

[...] The spin viewer window no longer hides behind the main relax window after the launch of the user

[...] function.

[...]........

[...] r17491 | bugman | 2012-09-18 19:23:14 +0200 (Tue, 18 Sep 2012) | 5 lines

[...]

[...] Added @HE1 to the spin ID list of the structure.load_spins user function.

[...]

[...] This is only seen in the GUI.

[...]........

[...] r17492 | bugman | 2012-09-18 19:44:54 +0200 (Tue, 18 Sep 2012) | 6 lines

[...]

[...] Updated the model-free GUI auto-analysis buttons for multiple spin name types.

[...]

[...] The @H and @N names in the wizards behind the 'Dipolar relaxation', 'X isotope', and 'H isotope'

[...] buttons have been changed to @H* and @N* to support Trp NE1-HE1 atom pairs.

[...]........

[...] r17493 | bugman | 2012-09-19 09:19:54 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] Fix for bug #20181 - the GUI sequence editor window TypeError problem.

[...]

[...] This is the fix for the bug reported at https://gna.org/bugs/?20181.

[...]........

[...] r17494 | bugman | 2012-09-19 09:35:49 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Improvements to the descriptions of the structure.read_pdb user function arguments.

[...]........

[...] r17495 | bugman | 2012-09-19 09:37:07 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Improvements to the descriptions of the structure.read_xyz user function arguments.

[...]........

[...] r17496 | bugman | 2012-09-19 09:43:30 +0200 (Wed, 19 Sep 2012) | 7 lines

[...]

[...] Fix for bug #20182 (https://gna.org/bugs/?20182) - the sequence element window ordering issue.

[...]

[...] The sequence element window now has the parent wx.Window element set. This prevents the main relax

[...] window from being set as the parent and hence coming to the front after the sequence element window

[...] is launched from a user function window.

[...]........

[...] r17497 | bugman | 2012-09-19 10:02:13 +0200 (Wed, 19 Sep 2012) | 6 lines

[...]

[...] Fix for bug #20183 (https://gna.org/bugs/?20183) - the failure of the sequence editor window.

[...]

[...] The problem was that fields which could be either single values or lists (or tuples) of values were

[...] not properly handled.

[...]........

[...] r17498 | bugman | 2012-09-19 10:53:11 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] Modified the operation of the sequence GUI element to have access to the sequence editor window.

[...]

[...] This is to allow this GUI element to be blasted within the test suite.

[...]........

[...] r17499 | bugman | 2012-09-19 10:55:30 +0200 (Wed, 19 Sep 2012) | 7 lines

[...]

[...] Created the User_functions.test_structure_pdb_read GUI test for checking the sequence editor window.

[...]

[...] This new user function GUI testing class is to be used for testing out the special GUI elements not

[...] invoked within the unit testing. The test_structure_pdb_read() test specifically shows a number of

[...] failures of the sequence editor window.

[...]........

[...] r17500 | bugman | 2012-09-19 11:22:35 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Fixes for the User_functions.test_structure_pdb_read() GUI test.

[...]........

[...] r17501 | bugman | 2012-09-19 11:24:21 +0200 (Wed, 19 Sep 2012) | 7 lines

[...]

[...] Fix for bug #20184 (https://gna.org/bugs/?20184).

[...]

[...] The behaviour of the gui.string_conv.gui_to_int() and related functions has changed in the last few

[...] months and the Sequence_window() GUI element has not changed to match. This has been fixed and the

[...] User_functions.test_structure_pdb_read() GUI test now passes.

[...]........

[...] r17502 | bugman | 2012-09-19 11:27:52 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] Modified the User_functions.test_structure_pdb_read() GUI test to catch another bug.

[...]

[...] This is a bug recently introduced with the fixes to the other sequence editor GUI window problems.

[...]........

[...] r17503 | bugman | 2012-09-19 11:38:56 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Small fix for the User_functions.test_structure_pdb_read() GUI test.

[...]........

[...] r17504 | bugman | 2012-09-19 11:40:28 +0200 (Wed, 19 Sep 2012) | 6 lines

[...]

[...] Another bug fix for the sequence GUI editor window.

[...]

[...] This bug was being triggered by the User_functions.test_structure_pdb_read() GUI test which now

[...] passes.

[...]........

[...] r17505 | bugman | 2012-09-19 14:16:04 +0200 (Wed, 19 Sep 2012) | 6 lines

[...]

[...] Fix for bug #20177 (https://gna.org/bugs/?20177).

[...]

[...] This was simply a lower precision OS/Python/numpy combination causing a test suite failure - there

[...] are no practical effects and only the precision of the system/GUI test has been lowered.

[...]........

[...] r17506 | bugman | 2012-09-19 14:55:33 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] All of the GUI strings and text are now formatted with a small sans serif font in the user manual.

[...]

[...] This is because in the GUI, a sans serif font is almost always used be default.

[...]........

[...] r17507 | bugman | 2012-09-19 14:57:03 +0200 (Wed, 19 Sep 2012) | 6 lines

[...]

[...] Updated the data model chapter of the user manual to cover the handling of protons.

[...]

[...] This change includes the modification of the PDB reading screenshot to demonstrate the reading of a

[...] specific model and the naming of the molecule.

[...]........

[...] r17508 | bugman | 2012-09-19 15:42:33 +0200 (Wed, 19 Sep 2012) | 6 lines

[...]

[...] A number of updates and edits to the intro chapter of the user manual.

[...]

[...] The model-free GUI screenshot has been shifted to the intro chapter in preparation for a full

[...] tutorial with screenshots in the model-free chapter.

[...]........

[...] r17509 | bugman | 2012-09-19 15:43:04 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Added some labelling to the infrastructure chapter of the user manual for referencing.

[...]........

[...] r17510 | bugman | 2012-09-19 15:49:35 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] A small edit to the intro chapter for the multi-processor operation and logging.

[...]........

[...] r17511 | bugman | 2012-09-19 16:19:47 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Additions to the scripting section of the relaxation curve-fitting chapter of the user manual.

[...]........

[...] r17512 | bugman | 2012-09-19 16:57:35 +0200 (Wed, 19 Sep 2012) | 7 lines

[...]

[...] Created a simple shell script to find duplicate titles in the relax user manual.

[...]

[...] This is important for the HTML version of the manual as duplicated titles causes HTML pages to be

[...] overwritten. For example all chapters, sections and subsections titled "Introduction" will load the

[...] introduction.html file which will contain the text of the last section with that title!

[...]........

[...] r17513 | bugman | 2012-09-19 17:03:20 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Improvements to the duplicate user manual title finding script.

[...]........

[...] r17514 | bugman | 2012-09-19 17:22:47 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Fix for the duplicate title finding script - the LaTeX and HTML mode alternatives are no longer mixed up.

[...]........

[...] r17515 | bugman | 2012-09-19 17:25:16 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] The HTML files for the user manual now have longer names - this is needed for removing the duplicates.

[...]........

[...] r17516 | bugman | 2012-09-19 17:33:55 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] Elimination of all duplicated chapter, section and subsection titles in the user manual.

[...]

[...] This fixes bug #20185 (https://gna.org/bugs/?20185).

[...]........

[...] r17517 | bugman | 2012-09-19 18:41:08 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] The graphics.fetch_icon() function argument 'format' can now be set to None.

[...]

[...] This will return the file path without the extension.

[...]........

[...] r17518 | bugman | 2012-09-19 19:03:48 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Fix for the graphics.fetch_icon() function for when no file format is specified.

[...]........

[...] r17519 | bugman | 2012-09-19 21:49:04 +0200 (Wed, 19 Sep 2012) | 6 lines

[...]

[...] Removed the text '.eps.gz' from all of the LaTeX included graphics in the user manual.

[...]

[...] This allows latex2html to select and use the PNG images instead, producing much better graphics for

[...] the online manual (http://www.nmr-relax.com/manual/index.html).

[...]........

[...] r17520 | bugman | 2012-09-19 22:29:43 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] Fixes for the user function icons in the HTML version of the user manual.

[...]

[...] These icons are now placed on the correct HTML page.

[...]........

[...] r17521 | bugman | 2012-09-19 22:30:27 +0200 (Wed, 19 Sep 2012) | 3 lines

[...]

[...] Fixed a section titled 'Introduction' clashing with the intro chapter of the user manual.

[...]........

[...] r17522 | bugman | 2012-09-19 22:46:36 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] The latex2html compilation of the user manual now ignores the \bibitem{} commands.

[...]

[...] This is needed for the HTML version of the user manual.

[...]........

[...] r17523 | bugman | 2012-09-19 22:47:29 +0200 (Wed, 19 Sep 2012) | 5 lines

[...]

[...] The citations chapter is now included in the HTML version of the user manual.

[...]

[...] For some reason, a file named 'cite.tex' cannot be handled by latex2html.

[...]........

[...] r17524 | bugman | 2012-09-20 11:41:19 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Modified the dauvergne_protocol sample script to handle tryptophan indole NE1 data.

[...]........

[...] r17525 | bugman | 2012-09-20 12:08:11 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Added a section label to the intro chapter of the user manual.

[...]........

[...] r17526 | bugman | 2012-09-20 12:09:59 +0200 (Thu, 20 Sep 2012) | 5 lines

[...]

[...] Removed \verb from the \newcommand definitions as that is forbidden in LaTeX.

[...]

[...] Now Python code is formatted using a small TT font.

[...]........

[...] r17527 | bugman | 2012-09-20 12:11:11 +0200 (Thu, 20 Sep 2012) | 6 lines

[...]

[...] Removed the \pycodestar{} references in the development chapter.

[...]

[...] This command has been deleted as \newcommand cannot have \verb inside it! The \pycodestar{x}

[...] references have been changed to \verb*!x!.

[...]........

[...] r17528 | bugman | 2012-09-20 12:14:31 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Spacing fix.

[...]........

[...] r17529 | bugman | 2012-09-20 12:21:46 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Added a subsubsection label to the data model chapter of the user manual.

[...]........

[...] r17530 | bugman | 2012-09-20 16:34:18 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Created the User_functions.test_value_set GUI test demonstrating the failure of the value.set user function.

[...]........

[...] r17531 | bugman | 2012-09-20 17:21:44 +0200 (Thu, 20 Sep 2012) | 5 lines

[...]

[...] Fix for bug #20189 (https://gna.org/bugs/?20189).

[...]

[...] The Sequence GUI element can no handle values of None.

[...]........

[...] r17532 | bugman | 2012-09-20 17:39:30 +0200 (Thu, 20 Sep 2012) | 6 lines

[...]

[...] The GUI model-free auto-analysis dipole_pair.define field values have been changed again.

[...]

[...] These now default to @N and @H, as @N* and @H* will connect @N spins to @HE1 spins and @H spins to

[...] @NE1 spins!

[...]........

[...] r17533 | bugman | 2012-09-20 17:46:26 +0200 (Thu, 20 Sep 2012) | 5 lines

[...]

[...] Fixed the dipole_pair.define user function calls in the dauvergne_protocol.py sample script.

[...]

[...] This is a recently introduced problem only present in the trunk.

[...]........

[...] r17534 | bugman | 2012-09-20 20:32:32 +0200 (Thu, 20 Sep 2012) | 7 lines

[...]

[...] Massive expansion of the model-free chapter of the user manual including script and GUI tutorials.

[...]

[...] The model-free chapter now has step-by-step tutorials for both the prompt/script mode and GUI mode

[...] for the new automated model-free protocol (the d'Auvergne protocol). This includes a large set of

[...] screenshots for the GUI mode.

[...]........

[...] r17535 | bugman | 2012-09-20 20:47:09 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Added a BMRB section to the end of the model-free chapter of the user manual.

[...]........

[...] r17536 | bugman | 2012-09-20 20:49:02 +0200 (Thu, 20 Sep 2012) | 3 lines

[...]

[...] Removed the out of date and useless README file for the HTML version of the user manual.

[...]........

[...] r17537 | bugman | 2012-09-21 10:22:46 +0200 (Fri, 21 Sep 2012) | 3 lines

[...]

[...] Added the use of the program 'nice' to the model-free GUI tutorial in the user manual.

[...]........

[...] r17538 | bugman | 2012-09-21 11:09:52 +0200 (Fri, 21 Sep 2012) | 6 lines

[...]

[...] Modified the model-free optimisation final printout to be more multi-processor friendly.

[...]

[...] The message saying that the optimised chi2 is an improvement or not now includes the spin ID string

[...] if present. This is more informative for the multi-processor mpi4py printouts.

[...]........

[...]

[...]

(Browse SVN revision 17828)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 19 Sep 2012 03:33:55 PM UTC, SVN revision 17516:

Elimination of all duplicated chapter, section and subsection titles in the user manual.

This fixes bug #20185 (https://gna.org/bugs/?20185).

(Browse SVN revision 17516)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Wed 19 Sep 2012 03:33:33 PM UTC, original submission:

The online version of the relax user manual is broken. Replicated chapter, section and subsection titles result in the same file being created for each. The file contents will be the last section with the replicated title. For example clicking on the Introduction chapter link at http://www.nmr-relax.com/manual/index.html will go to the page http://www.nmr-relax.com/manual/Introduction.html which is currently the introduction for the 'Values, gradients, and Hessians' chapter!

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

No files currently attached

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 2 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Wed 19 Sep 2012 03:34:38 PM UTCbugmanStatusNone=>Fixed
      Open/ClosedOpen=>Closed
    Show feedback again

    Back to the top


    Powered by Savane 3.1-cleanup